data_4YXD # _model_server_result.job_id mviZi39ZMBsTWFFienvXDA _model_server_result.datetime_utc '2024-11-24 10:00:02' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4yxd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":301}' # _entry.id 4YXD # _exptl.entry_id 4YXD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 616.487 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PROTOPORPHYRIN IX CONTAINING FE' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 4YXD _cell.length_a 70.366 _cell.length_b 83.746 _cell.length_c 292.625 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YXD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 9 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 B SG CYS 93 B CYS 65 1_555 F FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc2 B SG CYS 98 B CYS 70 1_555 F FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc3 B SG CYS 101 B CYS 73 1_555 F FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc4 B SG CYS 113 B CYS 85 1_555 F FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc5 B SG CYS 186 B CYS 158 1_555 G FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc6 B SG CYS 189 B CYS 161 1_555 G FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc7 B SG CYS 192 B CYS 164 1_555 G FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.806 ? metalc ? metalc8 B SG CYS 196 B CYS 168 1_555 H FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc9 B SG CYS 243 B CYS 215 1_555 H FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc10 B SG CYS 249 B CYS 221 1_555 H FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc11 B SG CYS 253 B CYS 225 1_555 G FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc12 C NE2 HIS 127 C HIS 101 1_555 I FE HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc13 I FE HEM . C HEM 301 1_555 D NE2 HIS 102 D HIS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? # _chem_comp.formula 'C34 H32 Fe N4 O4' _chem_comp.formula_weight 616.487 _chem_comp.id HEM _chem_comp.mon_nstd_flag . _chem_comp.name 'PROTOPORPHYRIN IX CONTAINING FE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms HEME # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag CHA C1A HEM sing 273 n n CHA C4D HEM doub 274 n n CHA HHA HEM sing 275 n n CHB C4A HEM sing 276 n n CHB C1B HEM doub 277 n n CHB HHB HEM sing 278 n n CHC C4B HEM sing 279 n n CHC C1C HEM doub 280 n n CHC HHC HEM sing 281 n n CHD C4C HEM doub 282 n n CHD C1D HEM sing 283 n n CHD HHD HEM sing 284 n n C1A C2A HEM doub 285 n y C1A NA HEM sing 286 n y C2A C3A HEM sing 287 n y C2A CAA HEM sing 288 n n C3A C4A HEM doub 289 n y C3A CMA HEM sing 290 n n C4A NA HEM sing 291 n y CMA HMA HEM sing 292 n n CMA HMAA HEM sing 293 n n CMA HMAB HEM sing 294 n n CAA CBA HEM sing 295 n n CAA HAA HEM sing 296 n n CAA HAAA HEM sing 297 n n CBA CGA HEM sing 298 n n CBA HBA HEM sing 299 n n CBA HBAA HEM sing 300 n n CGA O1A HEM doub 301 n n CGA O2A HEM sing 302 n n C1B C2B HEM sing 303 n n C1B NB HEM sing 304 n n C2B C3B HEM doub 305 n n C2B CMB HEM sing 306 n n C3B C4B HEM sing 307 n n C3B CAB HEM sing 308 n n C4B NB HEM doub 309 n n CMB HMB HEM sing 310 n n CMB HMBA HEM sing 311 n n CMB HMBB HEM sing 312 n n CAB CBB HEM doub 313 n n CAB HAB HEM sing 314 n n CBB HBB HEM sing 315 n n CBB HBBA HEM sing 316 n n C1C C2C HEM sing 317 n y C1C NC HEM sing 318 n y C2C C3C HEM doub 319 n y C2C CMC HEM sing 320 n n C3C C4C HEM sing 321 n y C3C CAC HEM sing 322 n n C4C NC HEM sing 323 n y CMC HMC HEM sing 324 n n CMC HMCA HEM sing 325 n n CMC HMCB HEM sing 326 n n CAC CBC HEM doub 327 n n CAC HAC HEM sing 328 n n CBC HBC HEM sing 329 n n CBC HBCA HEM sing 330 n n C1D C2D HEM sing 331 n n C1D ND HEM doub 332 n n C2D C3D HEM doub 333 n n C2D CMD HEM sing 334 n n C3D C4D HEM sing 335 n n C3D CAD HEM sing 336 n n C4D ND HEM sing 337 n n CMD HMD HEM sing 338 n n CMD HMDA HEM sing 339 n n CMD HMDB HEM sing 340 n n CAD CBD HEM sing 341 n n CAD HAD HEM sing 342 n n CAD HADA HEM sing 343 n n CBD CGD HEM sing 344 n n CBD HBD HEM sing 345 n n CBD HBDA HEM sing 346 n n CGD O1D HEM doub 347 n n CGD O2D HEM sing 348 n n O2A H2A HEM sing 349 n n O2D H2D HEM sing 350 n n FE NA HEM sing 351 n n FE NB HEM sing 352 n n FE NC HEM sing 353 n n FE ND HEM sing 354 n n # _atom_sites.entry_id 4YXD _atom_sites.fract_transf_matrix[1][1] 0.014211 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011941 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.003417 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code E 5 FAD A 1 700 700 FAD FAD . F 6 FES B 1 301 302 FES FES . G 7 SF4 B 1 302 303 SF4 SF4 . H 8 F3S B 1 303 304 F3S F3S . I 9 HEM C 1 301 301 HEM HEM . J 10 FTN C 1 302 302 FTN FTN . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C CHA HEM . . . I 9 -32.84 -27.013 64.702 1 66.82 ? CHA HEM 301 C 1 HETATM 2 C CHB HEM . . . I 9 -36.795 -24.333 65.336 1 79.92 ? CHB HEM 301 C 1 HETATM 3 C CHC HEM . . . I 9 -36.962 -25.686 70.004 1 82.31 ? CHC HEM 301 C 1 HETATM 4 C CHD HEM . . . I 9 -33.359 -28.754 69.199 1 70.68 ? CHD HEM 301 C 1 HETATM 5 C C1A HEM . . . I 9 -33.885 -26.173 64.479 1 72.56 ? C1A HEM 301 C 1 HETATM 6 C C2A HEM . . . I 9 -34.285 -25.712 63.196 1 75.32 ? C2A HEM 301 C 1 HETATM 7 C C3A HEM . . . I 9 -35.403 -24.966 63.381 1 74.6 ? C3A HEM 301 C 1 HETATM 8 C C4A HEM . . . I 9 -35.697 -24.964 64.766 1 75.98 ? C4A HEM 301 C 1 HETATM 9 C CMA HEM . . . I 9 -36.189 -24.258 62.305 1 76.48 ? CMA HEM 301 C 1 HETATM 10 C CAA HEM . . . I 9 -33.625 -25.99 61.858 1 78.74 ? CAA HEM 301 C 1 HETATM 11 C CBA HEM . . . I 9 -32.743 -24.826 61.398 1 82.68 ? CBA HEM 301 C 1 HETATM 12 C CGA HEM . . . I 9 -31.908 -25.218 60.198 1 83.01 ? CGA HEM 301 C 1 HETATM 13 O O1A HEM . . . I 9 -30.793 -25.764 60.358 1 79.29 ? O1A HEM 301 C 1 HETATM 14 O O2A HEM . . . I 9 -32.319 -24.985 59.04 1 85.49 ? O2A HEM 301 C 1 HETATM 15 C C1B HEM . . . I 9 -37.19 -24.461 66.685 1 79.03 ? C1B HEM 301 C 1 HETATM 16 C C2B HEM . . . I 9 -38.296 -23.757 67.261 1 78.84 ? C2B HEM 301 C 1 HETATM 17 C C3B HEM . . . I 9 -38.346 -24.126 68.585 1 80.26 ? C3B HEM 301 C 1 HETATM 18 C C4B HEM . . . I 9 -37.229 -25.072 68.78 1 78.9 ? C4B HEM 301 C 1 HETATM 19 C CMB HEM . . . I 9 -39.215 -22.806 66.521 1 77.97 ? CMB HEM 301 C 1 HETATM 20 C CAB HEM . . . I 9 -39.281 -23.766 69.676 1 88.82 ? CAB HEM 301 C 1 HETATM 21 C CBB HEM . . . I 9 -40.379 -23.038 69.52 1 95.95 ? CBB HEM 301 C 1 HETATM 22 C C1C HEM . . . I 9 -36.01 -26.678 70.199 1 81.02 ? C1C HEM 301 C 1 HETATM 23 C C2C HEM . . . I 9 -35.857 -27.444 71.377 1 83.55 ? C2C HEM 301 C 1 HETATM 24 C C3C HEM . . . I 9 -34.813 -28.34 71.14 1 79.69 ? C3C HEM 301 C 1 HETATM 25 C C4C HEM . . . I 9 -34.366 -28.091 69.809 1 73.07 ? C4C HEM 301 C 1 HETATM 26 C CMC HEM . . . I 9 -36.678 -27.304 72.644 1 82.94 ? CMC HEM 301 C 1 HETATM 27 C CAC HEM . . . I 9 -34.233 -29.375 72.033 1 80.57 ? CAC HEM 301 C 1 HETATM 28 C CBC HEM . . . I 9 -34.651 -29.637 73.268 1 81.47 ? CBC HEM 301 C 1 HETATM 29 C C1D HEM . . . I 9 -32.977 -28.471 67.901 1 70.72 ? C1D HEM 301 C 1 HETATM 30 C C2D HEM . . . I 9 -31.845 -29.189 67.32 1 70.42 ? C2D HEM 301 C 1 HETATM 31 C C3D HEM . . . I 9 -31.703 -28.705 66.08 1 67.12 ? C3D HEM 301 C 1 HETATM 32 C C4D HEM . . . I 9 -32.738 -27.684 65.902 1 68.23 ? C4D HEM 301 C 1 HETATM 33 C CMD HEM . . . I 9 -30.989 -30.251 67.958 1 72.78 ? CMD HEM 301 C 1 HETATM 34 C CAD HEM . . . I 9 -30.666 -29.126 65.082 1 61.85 ? CAD HEM 301 C 1 HETATM 35 C CBD HEM . . . I 9 -29.504 -28.134 65.086 1 57.09 ? CBD HEM 301 C 1 HETATM 36 C CGD HEM . . . I 9 -28.932 -27.94 63.695 1 57.48 ? CGD HEM 301 C 1 HETATM 37 O O1D HEM . . . I 9 -29.343 -28.533 62.665 1 55.17 ? O1D HEM 301 C 1 HETATM 38 O O2D HEM . . . I 9 -27.99 -27.141 63.561 1 60.82 ? O2D HEM 301 C 1 HETATM 39 N NA HEM . . . I 9 -34.769 -25.725 65.433 1 74.34 ? NA HEM 301 C 1 HETATM 40 N NB HEM . . . I 9 -36.597 -25.192 67.622 1 73.49 ? NB HEM 301 C 1 HETATM 41 N NC HEM . . . I 9 -35.085 -27.073 69.274 1 73.54 ? NC HEM 301 C 1 HETATM 42 N ND HEM . . . I 9 -33.472 -27.563 67.029 1 71.96 ? ND HEM 301 C 1 HETATM 43 FE FE HEM . . . I 9 -34.977 -26.443 67.288 1 69.19 ? FE HEM 301 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 470 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 43 #